Environmental Microbiology, Volume 14, Issue 1, January 2012 VOLUME 14 NUMBER 1 JANUARY 2012 www.env-micro.com ISSN 1462-2912 Contents environmental microbiology Correspondence 140 Microbial rhodopsins on leaf surfaces of terrestrial plants N. Atamna-Ismaeel, O. M. Finkel, F. Glaser, I. Sharon, R. Schneider, 1 Omics for understanding microbial functional dynamics A. F. Post, J. L. Spudich, C. von Mering, J. A. Vorholt, D. Iluz, O. Béjà & J. K. Jansson, J. D. Neufeld, M. A. Moran & J. A. Gilbert S. Belkin 147 Photoautotrophic symbiont and geography are major factors affecting highly Minireviews structured and diverse bacterial communities in the lichen microbiome 4 Beyond the Venn diagram: the hunt for a core microbiome B. P. Hodkinson, N. R. Gottel, C. W. Schadt & F. Lutzoni A. Shade & J. Handelsman 162 Phosphate transporters in marine phytoplankton and their viruses: environmental cross-domain commonalities in viral-host gene exchanges 13 Targeted metagenomics: a high-resolution metagenomics approach for specifi c A. Monier, R. M. Welsh, C. Gentemann, G. Weinstock, E. Sodergren, gene clusters in complex microbial communities E. V. Armbrust, J. A. Eisen & A. Z. Worden H. Suenaga 177 Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the phylum Acidobacteria Research articles A. M. Garcia Costas, Z. Liu, L. P. Tomsho, S. C. Schuster, D. M. Ward & 23 Microbial metatranscriptomics in a permanent marine oxygen minimum zone D. A. Bryant F. J. Stewart, O. Ulloa & E. F. DeLong 191 Transcriptional responses of surface water marine microbial assemblages 41 Genome content of uncultivated marine Roseobacters in the surface ocean to deep-sea water amendment microbiology H. Luo, A. Löytynoja & M. A. Moran Y. Shi, J. McCarren & E. F. DeLong 207 Phage–bacteria relationships and CRISPR elements revealed by a 52 Genomic content of uncultured Bacteroidetes from contrasting oceanic metagenomic survey of the rumen microbiome provinces in the North Atlantic Ocean M. E. Berg Miller, C. J. Yeoman, N. Chia, S. G. Tringe, F. E. Angly, P. R. Gómez-Pereira, M. Schüler, B. M. Fuchs, C. Bennke, H. Teeling, R. A. Edwards, H. J. Flint, R. Lamed, E. A. Bayer & B. A. White J. Waldmann, M. Richter, V. Barbe, E. Bataille, F. O. Glöckner & R. Amann 228 Bacterial community transcription patterns during a marine phytoplankton bloom VOLUME 14 67 Whole-genome expression analysis reveals a role for death-related genes in J. M. Rinta-Kanto, S. Sun, S. Sharma, R. P. Kiene & M. A. Moran stress acclimation of the diatom Thalassiosira pseudonana 240 Metagenomic comparison of microbial communities inhabiting confi ned and K. Thamatrakoln, O. Korenovska, A. K. Niheu & K. D. Bidle unconfi ned aquifer ecosystems 82 Comparative microbial diversity analyses of modern marine thrombolitic mats R. J. Smith, T. C. Jeffries, B. Roudnew, A. J. Fitch, J. R. Seymour, by barcoded pyrosequencing M. W. Delpin, K. Newton, M. H. Brown & J. G. Mitchell J. M. Mobberley, M. C. Ortega & J. S. Foster 254 Metagenomic analysis of a complex marine planktonic thaumarchaeal community from the Gulf of Maine 101 The genome sequence of Desulfatibacillum alkenivorans AK-01: a blueprint for B. J. Tully, W. C. Nelson & J. F. Heidelberg anaerobic alkane oxidation NUMBER 1 A. V. Callaghan, B. E. L. Morris, I. A. C. Pereira, M. J. McInerney, 268 Unveiling microbial life in the new deep-sea hypersaline Lake Thetis. Part II: R. N. Austin, J. T. Groves, J. J. Kukor, J. M. Sufl ita, L. Y. Young, a metagenomic study G. J. Zylstra & B. Wawrik M. Ferrer, J. Werner, T. N. Chernikova, R. Bargiela, L. Fernández, V. La Cono, J. Waldmann, H. Teeling, O. V. Golyshina, F. O. Glöckner, 114 Iron transporters in marine prokaryotic genomes and metagenomes M. M. Yakimov & P. N. Golyshin B. M. Hopkinson & K. A. Barbeau Web alert 129 Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools 282 Microbial omics R. W. Li, E. E. Connor, C. Li, R. L. Baldwin, VI & M. E. Sparks L. P. Wackett PAGES 1–284 Forthcoming papers JANUARY 2012 Environmental Microbiology Environmental Microbiology Reports Minireview Minireview Marine sponges and their microbial symbionts: love and other relationships Local and regional factors infl uencing bacterial community assembly N. S. Webster & M. W. Taylor E. S. Lindström & S. Langenheder Research articles Multilocus sequence analysis, taxonomic resolution and biogeography of marine Brief reports Synechococcus Repeated sampling reveals differential variability in measures of species richness S. Mazard, M. Ostrowski, F. Partensky & D. J. Scanlan and community composition in planktonic protists Massive dominance of Epsilonproteobacteria in formation waters from a Canadian J. R. Dolan & T. Stoeck oil sands reservoir containing severely biodegraded oil C. R. J. Hubert, T. B. P. Oldenburg, M. Fustic, N. D. Gray, S. R. Larter, K. Penn, Age, sun and substrate: triggers of bacterial communities in lichens A. K. Rowan, R. Seshadri, A. Sherry, R. Swainsbury, G. Voordouw, J. K. Voordouw M. Cardinale, J. Steinová, J. Rabensteiner, G. Berg & M. Grube & I. M. Head Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria A novel genus of multicellular magnetotactic prokaryotes from the Yellow Sea are low GC K. Zhou, W.-Y. Zhang, K. Yu-Zhang, H.-M. Pan, S.-D. Zhang, W.-J. Zhang, R. Ghai, K. D. McMahon & F. Rodriguez-Valera H.-D. Yue, Y. Li, T. Xiao & L.-F. Wu Correlative microscopy for phylogenetic and ultrastructural characterization Prokaryotic taxonomy in the sequencing era – the polyphasic approach revisited of microbial communities P. Kämpfer & S. P. Glaeser B. Knierim, B. Luef, P. Wilmes, R. I. Webb, M. Auer, L. R. Comolli & J. F. Banfi eld OMICS Driven Microbial Ecology Hunt for a core microbiome This Journal is indexed by Index Medicus, SciSearch, ISI High-resolution metagenomics of specifi c gene clusters Alerting Services, Biotechnology Citation Index, Current Contents/Life Sciences, and Current Contents/Agriculture, Biology and Environmental Sciences. Iron transporters in metagenomes This journal is available online at Wiley Online Library. CRISPR elements in the rumen microbiome Visit http://wileyonlinelibrary.com/ to search the articles and register for table of contents e-mail alerts. Published jointly by the Society for Applied Microbiology and Blackwell Publishing Ltd. 001_emi_v14_i1_8.7mm_OC.indd 1 12/23/2011 2:42:47 PM Environmental Microbiology (2012) 14(1), 82–100 doi:10.1111/j.1462-2920.2011.02509.x Comparative microbial diversity analyses of modern marine thrombolitic mats by barcoded pyrosequencing Jennifer M. Mobberley, Maya C. Ortega and Introduction Jamie S. Foster* Microbialites are carbonate build-ups that are derived Department of Microbiology and Cell Science, University from the trapping, binding and mineral precipitation activi- of Florida, Space Life Sciences Laboratory, Kennedy ties of microbial mat communities (Burne and Moore, Space Center, FL 32899, USA. 1987). Microbialites are found across the globe in a wide variety of aquatic habitats (e.g. freshwater, hypersaline, Summaryemi_2509 82..100 marine) and represent one of the oldest known ecosys- tems on the planet (Canfield and DesMarais, 1993; Grotz- Thrombolites are unlaminated carbonate structures inger and Knoll, 1999). Microbialites are classified by their that form as a result of the metabolic interactions of internal micro- and mesostructure, which can range from complex microbial mat communities. Thrombolites the well-laminated stromatolites to the unlaminated, have a long geological history; however, little is clotted thrombolites (Kennard and James, 1986). One of known regarding the microbes associated with the few modern sites where both stromatolites and throm- modern structures. In this study, we use a barcoded bolites are actively forming is the island of Highborne Cay 16S rRNA gene-pyrosequencing approach coupled located in the Exuma Sound, Bahamas (Dravis, 1983; Dill with morphological analysis to assess the bacterial, et al., 1986; Reid et al., 2000). Considerable progress has cyanobacterial and archaeal diversity associated with been made on understanding the microbiological, geo- actively forming thrombolites found in Highborne logical and biogeochemical processes associated with the Cay, Bahamas. Analyses revealed four distinct micro- stromatolitic microbialites of Highborne Cay (Reid et al., bial mat communities referred to as black, beige, pink 2000; Visscher et al., 2000; Havemann and Foster, 2008; and button mats on the surfaces of the thrombolites. Baumgartner et al., 2009; Dupraz et al., 2009; Foster At a coarse phylogenetic resolution, the domain bac- et al., 2009; Foster and Green, 2011). However, far less terial sequence libraries from the four mats were progress has been made on understanding similar pro- similar, with Proteobacteria and Cyanobacteria being cesses in the adjacent, unlaminated thrombolitic microbi- the most abundant. At the finer resolution of the rRNA alites (Planavsky et al., 2009; Myshrall et al., 2010). gene sequences, significant differences in commu- Initial work by Myshrall and colleagues (2010) provided nity structure were observed, with dramatically differ- the first assessment of the microbial communities associ- ent cyanobacterial communities. Of the four mat ated with the thrombolite structures of Highborne Cay. types, the button mats contained the highest diversity This previous study generated clone libraries to the 16S of Cyanobacteria, and were dominated by two and 18S